chr6-31392656-A-G

Variant names:

• chr6-31392656-A-G
• rs7751725
• ENST00000744921.1:n.363A>G

Variant summary

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

The ENST00000744921.1(ENSG00000297040):​n.363A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,622 control chromosomes in the GnomAD database, including 7,975 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 (7975 hom., cov: 31)
• Consequence: ENSG00000297040 ENST00000744921.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 19 publications found

Genes affected

ENSG00000297040 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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
ENSG00000297040	ENST00000744921.1	n.363A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297040	ENST00000744920.1	n.120+3215A>G		intron_variant	Intron 1 of 2
MICA-AS1	ENST00000745027.1	n.567+7398T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47095 AN: 151504 Hom.: 7961 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.311 AC: 47153 AN: 151622 Hom.: 7975 Cov.: 31 AF XY: 0.316 AC XY: 23413 AN XY: 74090

African (AFR) AF: 0.365 AC: 15035 AN: 41232

American (AMR) AF: 0.358 AC: 5417 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1939 AN: 3460

East Asian (EAS) AF: 0.313 AC: 1612 AN: 5142

South Asian (SAS) AF: 0.303 AC: 1457 AN: 4802

European-Finnish (FIN) AF: 0.336 AC: 3546 AN: 10554

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16929 AN: 67984

Other (OTH) AF: 0.326 AC: 685 AN: 2104

Alfa AF: 0.271 Hom.: 13317

Bravo AF: 0.315

Asia WGS AF: 0.316 AC: 1099 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7751725; hg19: chr6-31360433; COSMIC: COSV74094117;