rs7749323

Variant names:

• chr6-137909252-G-A
• rs7749323

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0333 in 152,234 control chromosomes in the GnomAD database, including 95 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 0.033 (95 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0333 (5070/152234) while in subpopulation AFR AF = 0.0485 (2014/41540). AF 95% confidence interval is 0.0467. There are 95 homozygotes in GnomAd4. There are 2426 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 95 gene

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: 0.0333 AC: 5061 AN: 152116 Hom.: 95 Cov.: 32

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0414

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0333 AC: 5070 AN: 152234 Hom.: 95 Cov.: 32 AF XY: 0.0326 AC XY: 2426 AN XY: 74420

African (AFR) AF: 0.0485 AC: 2014 AN: 41540

American (AMR) AF: 0.0240 AC: 367 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3472

East Asian (EAS) AF: 0.0419 AC: 217 AN: 5182

South Asian (SAS) AF: 0.0363 AC: 175 AN: 4818

European-Finnish (FIN) AF: 0.0166 AC: 176 AN: 10608

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0282 AC: 1915 AN: 68012

Other (OTH) AF: 0.0279 AC: 59 AN: 2112

Alfa AF: 0.0323 Hom.: 25

Bravo AF: 0.0338

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.35
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs7749323; hg19: chr6-138230389;