chr7-34903208-T-C

Variant names:

• chr7-34903208-T-C
• rs4723388

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 0.18 in 152,172 control chromosomes in the GnomAD database, including 2,873 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 0.18 (2873 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.966
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.333 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: 0.180 AC: 27380 AN: 152054 Hom.: 2865 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.180 AC: 27400 AN: 152172 Hom.: 2873 Cov.: 32 AF XY: 0.187 AC XY: 13951 AN XY: 74410

African (AFR) AF: 0.143 AC: 5924 AN: 41524

American (AMR) AF: 0.341 AC: 5206 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3470

East Asian (EAS) AF: 0.217 AC: 1123 AN: 5170

South Asian (SAS) AF: 0.146 AC: 706 AN: 4830

European-Finnish (FIN) AF: 0.226 AC: 2398 AN: 10600

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11200 AN: 67984

Other (OTH) AF: 0.167 AC: 353 AN: 2114

Alfa AF: 0.169 Hom.: 11185

Bravo AF: 0.188

Asia WGS AF: 0.178 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.3
DANN	Benign	0.48
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs4723388; hg19: chr7-34942820;