chr6-31372834-G-T

Position:

• chr6-31372834-G-T

Variant summary

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

The ENST00000649421.1(ENSG00000285647):​n.275-2049G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 150,876 control chromosomes in the GnomAD database, including 4,479 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 0.22 (4479 hom., cov: 32)
• Consequence: ENST00000649421.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649421.1	n.275-2049G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33797 AN: 150768 Hom.: 4479 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.224 AC: 33810 AN: 150876 Hom.: 4479 Cov.: 32 AF XY: 0.231 AC XY: 16999 AN XY: 73608

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.244

Alfa AF: 0.204 Hom.: 719

Bravo AF: 0.223

Asia WGS AF: 0.331 AC: 1130 AN: 3406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.9
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7770216; hg19: chr6-31340611;