rs7627822

Variant names:

• chr3-138917970-A-C
• rs7627822

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 0.109 in 152,060 control chromosomes in the GnomAD database, including 1,343 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 0.11 (1343 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 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: 0.109 AC: 16534 AN: 151942 Hom.: 1339 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0835

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0554

Gnomad OTH AF: 0.0819

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

GnomAD4 genome AF: 0.109 AC: 16564 AN: 152060 Hom.: 1343 Cov.: 32 AF XY: 0.112 AC XY: 8325 AN XY: 74292

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.0577

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.0839

Gnomad4 SAS AF: 0.0662

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0553

Gnomad4 OTH AF: 0.0834

Alfa AF: 0.0953 Hom.: 99

Bravo AF: 0.109

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
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: rs7627822; hg19: chr3-138636812;