rs1342371

Positions:

• chr6-44772212-C-T

Variant summary

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

The ENST00000671451.1(ENSG00000286417):​n.159+44133C>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 0.11 in 152,292 control chromosomes in the GnomAD database, including 1,207 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 0.11 (1207 hom., cov: 33)
• Consequence: ENST00000671451.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929770	XR_926855.3	n.145-307C>T		intron_variant, non_coding_transcript_variant
LOC101929770	XR_007059596.1	n.252-307C>T		intron_variant, non_coding_transcript_variant
LOC101929770	XR_007059597.1	n.251+40844C>T		intron_variant, non_coding_transcript_variant
LOC101929770	XR_007059598.1	n.144+44133C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000671451.1	n.159+44133C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16782 AN: 152174 Hom.: 1209 Cov.: 33

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0517

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.110 AC: 16773 AN: 152292 Hom.: 1207 Cov.: 33 AF XY: 0.105 AC XY: 7833 AN XY: 74456

Gnomad4 AFR AF: 0.0326

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0516

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.131

Alfa AF: 0.156 Hom.: 1759

Bravo AF: 0.106

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342371; hg19: chr6-44739949;