6-31565601-G-A

Position:

• chr6-31565601-G-A

Variant summary

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

The NR_149045.1(LOC100287329):​n.122-4879C>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 0.643 in 151,904 control chromosomes in the GnomAD database, including 31,758 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 0.64 (31758 hom., cov: 30)
• Consequence: LOC100287329 NR_149045.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100287329	NR_149045.1	n.122-4879C>T		intron_variant, non_coding_transcript_variant
LTA	XM_047418773.1	c.-342+4332G>A		intron_variant			XP_047274729.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000691266.1	n.119-4879C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97569 AN: 151786 Hom.: 31723 Cov.: 30

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.643 AC: 97657 AN: 151904 Hom.: 31758 Cov.: 30 AF XY: 0.644 AC XY: 47787 AN XY: 74240

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.641

Alfa AF: 0.609 Hom.: 43279

Bravo AF: 0.641

Asia WGS AF: 0.617 AC: 2149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.69
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2857602; hg19: chr6-31533378;