rs910643

Variant names:

• chr4-3707278-C-T
• rs910643

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 0.336 in 152,084 control chromosomes in the GnomAD database, including 9,231 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 0.34 (9231 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 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: 0.336 AC: 51087 AN: 151966 Hom.: 9225 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.336 AC: 51124 AN: 152084 Hom.: 9231 Cov.: 32 AF XY: 0.336 AC XY: 24973 AN XY: 74334

African (AFR) AF: 0.225 AC: 9344 AN: 41510

American (AMR) AF: 0.307 AC: 4696 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3468

East Asian (EAS) AF: 0.120 AC: 621 AN: 5172

South Asian (SAS) AF: 0.387 AC: 1866 AN: 4820

European-Finnish (FIN) AF: 0.396 AC: 4183 AN: 10554

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27854 AN: 67952

Other (OTH) AF: 0.313 AC: 661 AN: 2112

Alfa AF: 0.380 Hom.: 1402

Bravo AF: 0.320

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs910643; hg19: chr4-3709005;