4-81228677-C-T

Variant names:

• chr4-81228677-C-T
• rs710841

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 0.365 in 151,916 control chromosomes in the GnomAD database, including 12,658 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 0.36 (12658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 38 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 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: 0.364 AC: 55310 AN: 151798 Hom.: 12629 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.365 AC: 55395 AN: 151916 Hom.: 12658 Cov.: 32 AF XY: 0.357 AC XY: 26511 AN XY: 74230

African (AFR) AF: 0.652 AC: 26977 AN: 41406

American (AMR) AF: 0.290 AC: 4421 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1088 AN: 3464

East Asian (EAS) AF: 0.183 AC: 944 AN: 5152

South Asian (SAS) AF: 0.223 AC: 1072 AN: 4812

European-Finnish (FIN) AF: 0.225 AC: 2381 AN: 10564

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.258 AC: 17520 AN: 67950

Other (OTH) AF: 0.323 AC: 681 AN: 2108

Alfa AF: 0.286 Hom.: 27693

Bravo AF: 0.383

Asia WGS AF: 0.219 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.6
DANN	Benign	0.77
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs710841; hg19: chr4-82149831;