16-46474032-G-T

Position:

• chr16-46474032-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026556.1(ANKRD26P1):​n.3531+217C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.971 in 215,636 control chromosomes in the GnomAD database, including 101,845 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 0.96 (70574 hom., cov: 29)
  • Exomes 𝑓: 0.99 (31271 hom.)
• Consequence: ANKRD26P1 NR_026556.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD26P1	NR_026556.1	n.3531+217C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000566201.6	n.3531+217C>A		intron_variant, non_coding_transcript_variant		1
	ENST00000571006.5	n.2153+217C>A		intron_variant, non_coding_transcript_variant		1
	ENST00000566933.5	n.240+217C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146191 AN: 151958 Hom.: 70546 Cov.: 29

Gnomad AFR AF: 0.868

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.987

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.974

GnomAD4 exome AF: 0.991 AC: 63011 AN: 63560 Hom.: 31271 AF XY: 0.993 AC XY: 33675 AN XY: 33914

Gnomad4 AFR exome AF: 0.861

Gnomad4 AMR exome AF: 0.991

Gnomad4 ASJ exome AF: 0.999

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.999

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.999

Gnomad4 OTH exome AF: 0.995

GnomAD4 genome AF: 0.962 AC: 146269 AN: 152076 Hom.: 70574 Cov.: 29 AF XY: 0.963 AC XY: 71575 AN XY: 74336

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.987

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 1.00

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 1.00

Gnomad4 OTH AF: 0.974

Alfa AF: 0.939 Hom.: 1824

Bravo AF: 0.956

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.7

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7197337; hg19: chr16-46507944;