6-40955671-C-T

Variant names:

• chr6-40955671-C-T
• rs991762
• ENST00000716633.1:n.374+45721G>A

Variant summary

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

The NR_110873.1(LOC101929555):​n.136-52973G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,054 control chromosomes in the GnomAD database, including 3,464 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 0.21 (3464 hom., cov: 32)
• Consequence: LOC101929555 NR_110873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 6 publications found

Genes affected

ENSG00000293636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_110873.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101929555	NR_110873.1		n.136-52973G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293636	ENST00000716633.1		n.374+45721G>A		intron	N/A
	ENSG00000293636	ENST00000740548.1		n.126-52973G>A		intron	N/A
	ENSG00000293636	ENST00000740549.1		n.584+42467G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32212 AN: 151936 Hom.: 3459 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.212 AC: 32254 AN: 152054 Hom.: 3464 Cov.: 32 AF XY: 0.214 AC XY: 15928 AN XY: 74324

African (AFR) AF: 0.217 AC: 8986 AN: 41450

American (AMR) AF: 0.216 AC: 3302 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1951 AN: 5132

South Asian (SAS) AF: 0.215 AC: 1034 AN: 4816

European-Finnish (FIN) AF: 0.207 AC: 2191 AN: 10582

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13303 AN: 67998

Other (OTH) AF: 0.227 AC: 478 AN: 2110

Alfa AF: 0.201 Hom.: 9780

Bravo AF: 0.214

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.80
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs991762; hg19: chr6-40923410;