rs75518195

Variant names:

• chr4-64201686-G-A
• rs75518195

Your query was ambiguous. Multiple possible variants found:

• chr4-64201686-G-A
• chr4-64201686-G-T

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 0.277 in 139,974 control chromosomes in the GnomAD database, including 5,705 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 0.28 (5705 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 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: 0.277 AC: 38724 AN: 139970 Hom.: 5706 Cov.: 27

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.277 AC: 38732 AN: 139974 Hom.: 5705 Cov.: 27 AF XY: 0.275 AC XY: 18705 AN XY: 67948

African (AFR) AF: 0.161 AC: 5792 AN: 35954

American (AMR) AF: 0.369 AC: 5197 AN: 14092

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 749 AN: 3410

East Asian (EAS) AF: 0.143 AC: 721 AN: 5038

South Asian (SAS) AF: 0.370 AC: 1674 AN: 4528

European-Finnish (FIN) AF: 0.249 AC: 2022 AN: 8130

Middle Eastern (MID) AF: 0.230 AC: 63 AN: 274

European-Non Finnish (NFE) AF: 0.330 AC: 21678 AN: 65742

Other (OTH) AF: 0.285 AC: 547 AN: 1922

Alfa AF: 0.297 Hom.: 733

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.065
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs75518195; hg19: chr4-65067404; COSMIC: COSV70325121;