6-140371171-C-G

Variant names:

• chr6-140371171-C-G
• rs1977772
• ENST00000684511.1:n.35+56237C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000684511.1(ENSG00000288714):​n.35+56237C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,240 control chromosomes in the GnomAD database, including 2,238 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 0.15 (2238 hom., cov: 33)
• Consequence: ENSG00000288714 ENST00000684511.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 2 publications found

Genes affected

ENSG00000288714 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000684511.1. 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
	ENSG00000288714	ENST00000684511.1		n.35+56237C>G		intron	N/A
	ENSG00000288714	ENST00000825769.1		n.370+7949C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22999 AN: 152122 Hom.: 2241 Cov.: 33

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.151 AC: 22986 AN: 152240 Hom.: 2238 Cov.: 33 AF XY: 0.150 AC XY: 11166 AN XY: 74424

African (AFR) AF: 0.0370 AC: 1537 AN: 41566

American (AMR) AF: 0.203 AC: 3104 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3470

East Asian (EAS) AF: 0.188 AC: 972 AN: 5182

South Asian (SAS) AF: 0.131 AC: 633 AN: 4828

European-Finnish (FIN) AF: 0.195 AC: 2067 AN: 10594

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13604 AN: 67986

Other (OTH) AF: 0.135 AC: 285 AN: 2116

Alfa AF: 0.0622 Hom.: 89

Bravo AF: 0.149

Asia WGS AF: 0.116 AC: 401 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.3
DANN	Benign	0.64
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1977772; hg19: chr6-140692308;