rs7801534

Variant names:

• chr7-49290084-A-G
• rs7801534

Variant summary

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

The variant allele was found at a frequency of 0.0946 in 152,182 control chromosomes in the GnomAD database, including 837 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 0.095 (837 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.842
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 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: 0.0945 AC: 14369 AN: 152064 Hom.: 836 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0845

Gnomad EAS AF: 0.0505

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0975

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

GnomAD4 genome AF: 0.0946 AC: 14392 AN: 152182 Hom.: 837 Cov.: 32 AF XY: 0.0943 AC XY: 7018 AN XY: 74412

African (AFR) AF: 0.157 AC: 6507 AN: 41494

American (AMR) AF: 0.107 AC: 1629 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0845 AC: 293 AN: 3466

East Asian (EAS) AF: 0.0496 AC: 257 AN: 5178

South Asian (SAS) AF: 0.0978 AC: 471 AN: 4818

European-Finnish (FIN) AF: 0.0388 AC: 411 AN: 10602

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0668 AC: 4541 AN: 68020

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.0776 Hom.: 1281

Bravo AF: 0.0989

Asia WGS AF: 0.127 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.67
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs7801534; hg19: chr7-49329680;