rs1908751

Variant names:

• chr7-45895920-C-T
• rs1908751

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 0.319 in 152,010 control chromosomes in the GnomAD database, including 7,904 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 0.32 (7904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48512 AN: 151892 Hom.: 7887 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.319 AC: 48555 AN: 152010 Hom.: 7904 Cov.: 32 AF XY: 0.327 AC XY: 24291 AN XY: 74300

African (AFR) AF: 0.312 AC: 12925 AN: 41422

American (AMR) AF: 0.301 AC: 4608 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1043 AN: 3472

East Asian (EAS) AF: 0.316 AC: 1632 AN: 5170

South Asian (SAS) AF: 0.323 AC: 1558 AN: 4822

European-Finnish (FIN) AF: 0.477 AC: 5040 AN: 10562

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20650 AN: 67960

Other (OTH) AF: 0.304 AC: 642 AN: 2112

Alfa AF: 0.306 Hom.: 12136

Bravo AF: 0.303

Asia WGS AF: 0.324 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.61
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1908751; hg19: chr7-45935519;