4-72917687-A-T

Variant names:

• chr4-72917687-A-T
• rs6816344

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 0.361 in 152,028 control chromosomes in the GnomAD database, including 10,788 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 (10788 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 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: 0.361 AC: 54821 AN: 151908 Hom.: 10755 Cov.: 33

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.361 AC: 54909 AN: 152028 Hom.: 10788 Cov.: 33 AF XY: 0.366 AC XY: 27180 AN XY: 74334

African (AFR) AF: 0.503 AC: 20841 AN: 41454

American (AMR) AF: 0.326 AC: 4979 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 867 AN: 3458

East Asian (EAS) AF: 0.510 AC: 2633 AN: 5164

South Asian (SAS) AF: 0.418 AC: 2011 AN: 4812

European-Finnish (FIN) AF: 0.331 AC: 3494 AN: 10570

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19042 AN: 67980

Other (OTH) AF: 0.322 AC: 678 AN: 2104

Alfa AF: 0.324 Hom.: 1043

Bravo AF: 0.363

Asia WGS AF: 0.425 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.46
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs6816344; hg19: chr4-73783404;