chr3-67213420-C-T

Variant names:

• chr3-67213420-C-T
• rs4857008

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 0.549 in 152,022 control chromosomes in the GnomAD database, including 23,139 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 0.55 (23139 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• 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 = 0.705 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: 0.549 AC: 83336 AN: 151902 Hom.: 23129 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.549 AC: 83395 AN: 152022 Hom.: 23139 Cov.: 32 AF XY: 0.544 AC XY: 40444 AN XY: 74300

African (AFR) AF: 0.532 AC: 22067 AN: 41464

American (AMR) AF: 0.629 AC: 9609 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1985 AN: 3468

East Asian (EAS) AF: 0.725 AC: 3744 AN: 5166

South Asian (SAS) AF: 0.472 AC: 2274 AN: 4818

European-Finnish (FIN) AF: 0.424 AC: 4477 AN: 10556

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37374 AN: 67960

Other (OTH) AF: 0.554 AC: 1169 AN: 2112

Alfa AF: 0.544 Hom.: 11558

Bravo AF: 0.566

Asia WGS AF: 0.567 AC: 1974 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	7.2
DANN	Benign	0.55
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs4857008; hg19: chr3-67263844;