6-14748444-T-C

Position:

• chr6-14748444-T-C

Variant summary

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

The ENST00000629853.2(ENSG00000234261):​n.313+41546A>G 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 0.821 in 152,074 control chromosomes in the GnomAD database, including 52,646 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 0.82 (52646 hom., cov: 31)
• Consequence: ENST00000629853.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000629853.2	n.313+41546A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000689305.1	n.179-7393A>G		intron_variant, non_coding_transcript_variant
	ENST00000702363.1	n.187-16966A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124797 AN: 151956 Hom.: 52634 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.821 AC: 124851 AN: 152074 Hom.: 52646 Cov.: 31 AF XY: 0.824 AC XY: 61261 AN XY: 74316

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.845

Alfa AF: 0.893 Hom.: 114373

Bravo AF: 0.804

Asia WGS AF: 0.896 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.63
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2472793; hg19: chr6-14748675;