rs79271207

Variant names:

• chr7-128913836-C-T
• rs2643764

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 0.16 in 1,489,608 control chromosomes in the GnomAD database, including 22,954 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 0.20 (3712 hom., cov: 31)
  • Exomes 𝑓: 0.16 (19242 hom.)
• Consequence: LOC392787 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 0 publications found

Genes affected

LOC392787 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000469533.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000224163	ENST00000469533.1	TSL:6	n.218+10G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30194 AN: 149630 Hom.: 3706 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0826

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.0983

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.156 AC: 208436 AN: 1339858 Hom.: 19242 Cov.: 22 AF XY: 0.158 AC XY: 106191 AN XY: 670872

African (AFR) AF: 0.268 AC: 7995 AN: 29858

American (AMR) AF: 0.162 AC: 7033 AN: 43366

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 3826 AN: 25274

East Asian (EAS) AF: 0.536 AC: 20052 AN: 37420

South Asian (SAS) AF: 0.219 AC: 18064 AN: 82410

European-Finnish (FIN) AF: 0.111 AC: 5721 AN: 51524

Middle Eastern (MID) AF: 0.160 AC: 658 AN: 4102

European-Non Finnish (NFE) AF: 0.134 AC: 135810 AN: 1010142

Other (OTH) AF: 0.166 AC: 9277 AN: 55762

GnomAD4 genome AF: 0.202 AC: 30218 AN: 149750 Hom.: 3712 Cov.: 31 AF XY: 0.198 AC XY: 14467 AN XY: 73074

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.290 AC: 11692 AN: 40384

American (AMR) AF: 0.151 AC: 2275 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 569 AN: 3446

East Asian (EAS) AF: 0.525 AC: 2574 AN: 4902

South Asian (SAS) AF: 0.237 AC: 1113 AN: 4690

European-Finnish (FIN) AF: 0.0983 AC: 1032 AN: 10496

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10456 AN: 67442

Other (OTH) AF: 0.184 AC: 383 AN: 2076

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.185 Hom.: 313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.23
DANN	Benign	0.50
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2643764; hg19: chr7-128553890; COSMIC: COSV52823237;