rs1257669

Variant names:

• chr14-99025855-G-A
• rs1257669
• ENST00000724621.1:n.207+10723C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000724621.1(ENSG00000294598):​n.207+10723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,008 control chromosomes in the GnomAD database, including 15,826 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 0.45 (15826 hom., cov: 33)
• Consequence: ENSG00000294598 ENST00000724621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 0 publications found

Genes affected

ENSG00000294598 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984696	XR_001750878.3	n.148-21086C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294598	ENST00000724621.1	n.207+10723C>T		intron_variant	Intron 1 of 4
ENSG00000294598	ENST00000724622.1	n.148-21086C>T		intron_variant	Intron 1 of 3
ENSG00000294598	ENST00000724623.1	n.155+10969C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68901 AN: 151888 Hom.: 15805 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.464

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.454 AC: 68963 AN: 152008 Hom.: 15826 Cov.: 33 AF XY: 0.455 AC XY: 33784 AN XY: 74320

African (AFR) AF: 0.505 AC: 20948 AN: 41456

American (AMR) AF: 0.488 AC: 7466 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1712 AN: 5146

South Asian (SAS) AF: 0.444 AC: 2140 AN: 4824

European-Finnish (FIN) AF: 0.490 AC: 5177 AN: 10558

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28820 AN: 67956

Other (OTH) AF: 0.464 AC: 977 AN: 2106

Alfa AF: 0.444 Hom.: 2657

Bravo AF: 0.455

Asia WGS AF: 0.390 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.51
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs1257669; hg19: chr14-99492192;