6-98124244-T-C

Position:

• chr6-98124244-T-C

Variant summary

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

The ENST00000656098.1(ENSG00000271860):​n.1400+24974T>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 0.41 in 151,948 control chromosomes in the GnomAD database, including 13,909 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 0.41 (13909 hom., cov: 31)
• Consequence: ENST00000656098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 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
	ENST00000656098.1	n.1400+24974T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62358 AN: 151830 Hom.: 13914 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.410 AC: 62353 AN: 151948 Hom.: 13909 Cov.: 31 AF XY: 0.407 AC XY: 30231 AN XY: 74246

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.414

Alfa AF: 0.444 Hom.: 1900

Bravo AF: 0.393

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10457441; hg19: chr6-98572120;