chr2-165955255-A-G

Variant names:

• chr2-165955255-A-G
• rs6731900

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 0.244 in 152,136 control chromosomes in the GnomAD database, including 5,092 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 0.24 (5092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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: 0.244 AC: 37070 AN: 152018 Hom.: 5094 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.244 AC: 37068 AN: 152136 Hom.: 5092 Cov.: 32 AF XY: 0.240 AC XY: 17820 AN XY: 74374

African (AFR) AF: 0.120 AC: 4984 AN: 41532

American (AMR) AF: 0.245 AC: 3748 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1301 AN: 3472

East Asian (EAS) AF: 0.127 AC: 656 AN: 5174

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4822

European-Finnish (FIN) AF: 0.237 AC: 2512 AN: 10578

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21530 AN: 67970

Other (OTH) AF: 0.298 AC: 629 AN: 2110

Alfa AF: 0.303 Hom.: 9199

Bravo AF: 0.240

Asia WGS AF: 0.185 AC: 643 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	2.7
DANN	Benign	0.68
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs6731900; hg19: chr2-166811765;