rs7738388

Variant names:

• chr6-141132008-T-C
• rs7738388

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 0.292 in 152,094 control chromosomes in the GnomAD database, including 6,698 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 0.29 (6698 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 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: 0.292 AC: 44445 AN: 151976 Hom.: 6710 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.292 AC: 44413 AN: 152094 Hom.: 6698 Cov.: 32 AF XY: 0.294 AC XY: 21820 AN XY: 74330

African (AFR) AF: 0.228 AC: 9462 AN: 41516

American (AMR) AF: 0.305 AC: 4653 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 847 AN: 3470

East Asian (EAS) AF: 0.383 AC: 1980 AN: 5164

South Asian (SAS) AF: 0.258 AC: 1241 AN: 4814

European-Finnish (FIN) AF: 0.354 AC: 3740 AN: 10568

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21512 AN: 67990

Other (OTH) AF: 0.286 AC: 604 AN: 2112

Alfa AF: 0.304 Hom.: 13142

Bravo AF: 0.286

Asia WGS AF: 0.318 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	15
DANN	Benign	0.80
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs7738388; hg19: chr6-141453145; COSMIC: COSV66239237;