rs6460071

Positions:

• chr7-74082866-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.152 in 549,304 control chromosomes in the GnomAD database, including 9,014 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 0.21 (4932 hom., cov: 32)
  • Exomes 𝑓: 0.13 (4082 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.74082866G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31892 AN: 152000 Hom.: 4907 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.0734

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.174

GnomAD4 exome AF: 0.129 AC: 51343 AN: 397186 Hom.: 4082 AF XY: 0.127 AC XY: 26542 AN XY: 208204

Gnomad4 AFR exome AF: 0.441

Gnomad4 AMR exome AF: 0.107

Gnomad4 ASJ exome AF: 0.0863

Gnomad4 EAS exome AF: 0.0852

Gnomad4 SAS exome AF: 0.132

Gnomad4 FIN exome AF: 0.102

Gnomad4 NFE exome AF: 0.126

Gnomad4 OTH exome AF: 0.134

GnomAD4 genome AF: 0.210 AC: 31961 AN: 152118 Hom.: 4932 Cov.: 32 AF XY: 0.207 AC XY: 15358 AN XY: 74372

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0781

Gnomad4 EAS AF: 0.0736

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.172

Alfa AF: 0.136 Hom.: 1790

Bravo AF: 0.220

Asia WGS AF: 0.123 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6460071; hg19: chr7-73497196;