rs744103

Positions:

• chr6-43837625-T-A
• chr6-43837625-T-C
• chr6-43837625-T-G

Variant summary

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

The ENST00000637813.1(ENSG00000283573):​n.366-4886T>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 0.592 in 152,120 control chromosomes in the GnomAD database, including 29,256 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 0.59 (29256 hom., cov: 33)
• Consequence: ENST00000637813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375069	XR_001744130.1	n.675+259A>T		intron_variant, non_coding_transcript_variant
LOC105375070	XR_007059588.1	n.193-4886T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000637813.1	n.366-4886T>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90074 AN: 152002 Hom.: 29252 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.592 AC: 90106 AN: 152120 Hom.: 29256 Cov.: 33 AF XY: 0.597 AC XY: 44400 AN XY: 74374

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.609

Alfa AF: 0.633 Hom.: 4003

Bravo AF: 0.582

Asia WGS AF: 0.727 AC: 2529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.3
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs744103; hg19: chr6-43805362;