rs988426

Variant names:

• chr7-85987553-T-C
• rs988426
• ENST00000757672.1:n.224-20952A>G

Variant summary

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

The ENST00000757672.1(ENSG00000298738):​n.224-20952A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 152,070 control chromosomes in the GnomAD database, including 29,804 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 0.60 (29804 hom., cov: 32)
• Consequence: ENSG00000298738 ENST00000757672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 2 publications found

Genes affected

ENSG00000298738 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298738	ENST00000757672.1	n.224-20952A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91883 AN: 151952 Hom.: 29748 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.605 AC: 91994 AN: 152070 Hom.: 29804 Cov.: 32 AF XY: 0.598 AC XY: 44459 AN XY: 74330

African (AFR) AF: 0.850 AC: 35261 AN: 41496

American (AMR) AF: 0.496 AC: 7580 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2026 AN: 3466

East Asian (EAS) AF: 0.425 AC: 2196 AN: 5162

South Asian (SAS) AF: 0.433 AC: 2086 AN: 4818

European-Finnish (FIN) AF: 0.524 AC: 5538 AN: 10572

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.518 AC: 35192 AN: 67980

Other (OTH) AF: 0.592 AC: 1246 AN: 2104

Alfa AF: 0.558 Hom.: 8306

Bravo AF: 0.617

Asia WGS AF: 0.469 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.5
DANN	Benign	0.52
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs988426; hg19: chr7-85616869;