chr4-6734638-G-A

Variant names:

• chr4-6734638-G-A
• rs7661864

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 0.355 in 152,016 control chromosomes in the GnomAD database, including 10,229 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 0.35 (10229 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 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: 0.355 AC: 53906 AN: 151898 Hom.: 10214 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.355 AC: 53960 AN: 152016 Hom.: 10229 Cov.: 32 AF XY: 0.348 AC XY: 25862 AN XY: 74292

African (AFR) AF: 0.507 AC: 21025 AN: 41436

American (AMR) AF: 0.321 AC: 4908 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1394 AN: 5172

South Asian (SAS) AF: 0.338 AC: 1625 AN: 4814

European-Finnish (FIN) AF: 0.227 AC: 2393 AN: 10560

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20578 AN: 67970

Other (OTH) AF: 0.355 AC: 750 AN: 2112

Alfa AF: 0.324 Hom.: 23323

Bravo AF: 0.370

Asia WGS AF: 0.326 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.98
DANN	Benign	0.72
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7661864; hg19: chr4-6736365;