rs10487391

Variant names:

• chr7-118224974-G-A
• rs10487391
• NM_019644.4:c.144G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-118224974-G-A
• chr7-118224974-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_019644.4(ANKRD7):​c.144G>A​(p.Lys48Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0152 in 1,614,048 control chromosomes in the GnomAD database, including 509 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.018 (44 hom., cov: 31)
  • Exomes 𝑓: 0.015 (465 hom.)
• Consequence: ANKRD7 NM_019644.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

Genes affected

ANKRD7 (HGNC:18588): (ankyrin repeat domain 7) Predicted to act upstream of or within blastocyst hatching. Located in centrosome and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP7: Synonymous conserved (PhyloP=1.38 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD7	NM_019644.4	c.144G>A	p.Lys48Lys	synonymous_variant	Exon 1 of 7	ENST00000265224.9	NP_062618.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD7	ENST00000265224.9	c.144G>A	p.Lys48Lys	synonymous_variant	Exon 1 of 7	1	NM_019644.4	ENSP00000265224.4

Frequencies

GnomAD3 genomes AF: 0.0184 AC: 2793 AN: 152156 Hom.: 44 Cov.: 31

Gnomad AFR AF: 0.0188

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0415

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0773

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.00951

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00913

Gnomad OTH AF: 0.0182

GnomAD2 exomes AF: 0.0293 AC: 7239 AN: 247188 AF XY: 0.0255

Gnomad AFR exome AF: 0.0191

Gnomad AMR exome AF: 0.0931

Gnomad ASJ exome AF: 0.0228

Gnomad EAS exome AF: 0.0815

Gnomad FIN exome AF: 0.00728

Gnomad NFE exome AF: 0.00877

Gnomad OTH exome AF: 0.0240

GnomAD4 exome AF: 0.0149 AC: 21708 AN: 1461774 Hom.: 465 Cov.: 33 AF XY: 0.0148 AC XY: 10736 AN XY: 727194

Gnomad4 AFR exome AF: 0.0198 AC: 662 AN: 33470

Gnomad4 AMR exome AF: 0.0828 AC: 3702 AN: 44690

Gnomad4 ASJ exome AF: 0.0214 AC: 560 AN: 26128

Gnomad4 EAS exome AF: 0.0775 AC: 3076 AN: 39696

Gnomad4 SAS exome AF: 0.0250 AC: 2156 AN: 86250

Gnomad4 FIN exome AF: 0.00638 AC: 341 AN: 53412

Gnomad4 NFE exome AF: 0.00904 AC: 10049 AN: 1111970

Gnomad4 Remaining exome AF: 0.0161 AC: 970 AN: 60390

GnomAD4 genome AF: 0.0183 AC: 2793 AN: 152274 Hom.: 44 Cov.: 31 AF XY: 0.0198 AC XY: 1472 AN XY: 74468

Gnomad4 AFR AF: 0.0187 AC: 0.0186977 AN: 0.0186977

Gnomad4 AMR AF: 0.0416 AC: 0.0416231 AN: 0.0416231

Gnomad4 ASJ AF: 0.0199 AC: 0.0198962 AN: 0.0198962

Gnomad4 EAS AF: 0.0771 AC: 0.0771164 AN: 0.0771164

Gnomad4 SAS AF: 0.0288 AC: 0.0288262 AN: 0.0288262

Gnomad4 FIN AF: 0.00951 AC: 0.00950857 AN: 0.00950857

Gnomad4 NFE AF: 0.00910 AC: 0.0091016 AN: 0.0091016

Gnomad4 OTH AF: 0.0189 AC: 0.0189394 AN: 0.0189394

Alfa AF: 0.00622 Hom.: 40

Bravo AF: 0.0227

EpiCase AF: 0.0115

EpiControl AF: 0.0106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.43
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10487391; hg19: chr7-117865028; COSMIC: COSV54554948;