6-71688095-A-G

Variant names:

• chr6-71688095-A-G
• rs1321834
• ENST00000787970.1:n.1273A>G

Variant summary

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

The ENST00000787970.1(ENSG00000302585):​n.1273A>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 0.814 in 152,210 control chromosomes in the GnomAD database, including 50,644 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 0.81 (50644 hom., cov: 32)
• Consequence: ENSG00000302585 ENST00000787970.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 3 publications found

Genes affected

ENSG00000302585 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787970.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302585	ENST00000787970.1		n.1273A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000302585	ENST00000787971.1		n.682+470A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123845 AN: 152092 Hom.: 50609 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.814 AC: 123933 AN: 152210 Hom.: 50644 Cov.: 32 AF XY: 0.813 AC XY: 60497 AN XY: 74424

African (AFR) AF: 0.845 AC: 35113 AN: 41546

American (AMR) AF: 0.769 AC: 11765 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2979 AN: 3470

East Asian (EAS) AF: 0.635 AC: 3283 AN: 5170

South Asian (SAS) AF: 0.787 AC: 3795 AN: 4820

European-Finnish (FIN) AF: 0.837 AC: 8869 AN: 10594

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55551 AN: 68004

Other (OTH) AF: 0.801 AC: 1695 AN: 2116

Alfa AF: 0.802 Hom.: 2763

Bravo AF: 0.808

Asia WGS AF: 0.695 AC: 2418 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.39
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs1321834; hg19: chr6-72397798;