rs6460575

Variant names:

• chr7-70851379-G-A
• rs6460575

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 0.304 in 149,832 control chromosomes in the GnomAD database, including 7,806 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 0.30 (7806 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.4 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: 0.304 AC: 45563 AN: 149722 Hom.: 7808 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.304 AC: 45549 AN: 149832 Hom.: 7806 Cov.: 32 AF XY: 0.300 AC XY: 21940 AN XY: 73106

African (AFR) AF: 0.137 AC: 5614 AN: 40972

American (AMR) AF: 0.298 AC: 4472 AN: 15006

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1364 AN: 3446

East Asian (EAS) AF: 0.255 AC: 1266 AN: 4956

South Asian (SAS) AF: 0.279 AC: 1319 AN: 4724

European-Finnish (FIN) AF: 0.313 AC: 3188 AN: 10176

Middle Eastern (MID) AF: 0.517 AC: 150 AN: 290

European-Non Finnish (NFE) AF: 0.404 AC: 27216 AN: 67296

Other (OTH) AF: 0.324 AC: 670 AN: 2070

Alfa AF: 0.374 Hom.: 45041

Bravo AF: 0.290

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.63
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs6460575; hg19: chr7-70316365;