chr4-73662061-T-G

Variant names:

• chr4-73662061-T-G
• rs1247684

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 0.0276 in 152,328 control chromosomes in the GnomAD database, including 164 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 0.028 (164 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0788 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: 0.0275 AC: 4182 AN: 152210 Hom.: 160 Cov.: 32

Gnomad AFR AF: 0.0810

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0209

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00151

Gnomad OTH AF: 0.0263

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

GnomAD4 genome AF: 0.0276 AC: 4209 AN: 152328 Hom.: 164 Cov.: 32 AF XY: 0.0278 AC XY: 2069 AN XY: 74484

African (AFR) AF: 0.0811 AC: 3371 AN: 41550

American (AMR) AF: 0.0208 AC: 319 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3472

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5180

South Asian (SAS) AF: 0.0437 AC: 211 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10628

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00151 AC: 103 AN: 68044

Other (OTH) AF: 0.0317 AC: 67 AN: 2114

Alfa AF: 0.0216 Hom.: 15

Bravo AF: 0.0303

Asia WGS AF: 0.0640 AC: 222 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.64
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1247684; hg19: chr4-74527778;