rs988426

Variant names:

• chr7-85987553-T-C
• rs988426

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.592

Alfa AF: 0.556 Hom.: 4097

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs988426; hg19: chr7-85616869;