8-141622215-T-C

Position:

• chr8-141622215-T-C

Variant summary

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

The ENST00000673717.1(ENSG00000287677):​n.2021+9355T>C 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 0.771 in 152,226 control chromosomes in the GnomAD database, including 45,596 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 0.77 (45596 hom., cov: 34)
• Consequence: ENST00000673717.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000673717.1	n.2021+9355T>C		intron_variant, non_coding_transcript_variant
	ENST00000673759.1	n.2006+9355T>C		intron_variant, non_coding_transcript_variant
	ENST00000673982.1	n.1993+9355T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117221 AN: 152108 Hom.: 45542 Cov.: 34

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.771 AC: 117337 AN: 152226 Hom.: 45596 Cov.: 34 AF XY: 0.765 AC XY: 56958 AN XY: 74416

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.719

Alfa AF: 0.765 Hom.: 66123

Bravo AF: 0.767

Asia WGS AF: 0.626 AC: 2177 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13263959; hg19: chr8-142632315;