rs887780

Positions:

• chr6-139421651-G-A
• chr6-139421651-G-T

Variant summary

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

The ENST00000650173.1(ENSG00000226571):​n.510-7430G>A 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 0.701 in 152,120 control chromosomes in the GnomAD database, including 37,560 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 0.70 (37560 hom., cov: 33)
• Consequence: ENST00000650173.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986651	XR_001744382.1	n.105+1880G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650173.1	n.510-7430G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106623 AN: 152002 Hom.: 37535 Cov.: 33

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.701 AC: 106712 AN: 152120 Hom.: 37560 Cov.: 33 AF XY: 0.698 AC XY: 51915 AN XY: 74356

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.695

Alfa AF: 0.703 Hom.: 51048

Bravo AF: 0.706

Asia WGS AF: 0.635 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs887780; hg19: chr6-139742788;