rs1485004

Variant names:

• chr7-95641194-G-A
• rs1485004

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 0.313 in 151,918 control chromosomes in the GnomAD database, including 7,800 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 0.31 (7800 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 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: 0.313 AC: 47491 AN: 151800 Hom.: 7794 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.313 AC: 47518 AN: 151918 Hom.: 7800 Cov.: 31 AF XY: 0.319 AC XY: 23690 AN XY: 74236

African (AFR) AF: 0.270 AC: 11195 AN: 41410

American (AMR) AF: 0.262 AC: 3995 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1146 AN: 3470

East Asian (EAS) AF: 0.609 AC: 3136 AN: 5146

South Asian (SAS) AF: 0.520 AC: 2505 AN: 4818

European-Finnish (FIN) AF: 0.360 AC: 3794 AN: 10540

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20665 AN: 67954

Other (OTH) AF: 0.327 AC: 688 AN: 2106

Alfa AF: 0.311 Hom.: 32779

Bravo AF: 0.302

Asia WGS AF: 0.470 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.062
DANN	Benign	0.53
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1485004; hg19: chr7-95270506;