6-98124244-T-C

Variant names:

• chr6-98124244-T-C
• rs10457441
• ENST00000606913.5:n.240+24974T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000607032.1(ENSG00000271860):​n.410+24974T>C variant causes a intron 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: ENSG00000271860 ENST00000607032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 12 publications found

Genes affected

ENSG00000271860 (HGNC:58964):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607032.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000271860	ENST00000606913.5	TSL:5	n.240+24974T>C		intron	N/A
	ENSG00000271860	ENST00000607032.1	TSL:3	n.410+24974T>C		intron	N/A
	ENSG00000271860	ENST00000607823.5	TSL:5	n.352+24974T>C		intron	N/A

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

African (AFR) AF: 0.236 AC: 9794 AN: 41472

American (AMR) AF: 0.361 AC: 5511 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3470

East Asian (EAS) AF: 0.397 AC: 2047 AN: 5152

South Asian (SAS) AF: 0.293 AC: 1413 AN: 4824

European-Finnish (FIN) AF: 0.507 AC: 5344 AN: 10538

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35028 AN: 67916

Other (OTH) AF: 0.414 AC: 873 AN: 2108

Alfa AF: 0.483 Hom.: 24852

Bravo AF: 0.393

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.41
PhyloP100		-0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10457441;

hg19: chr6-98572120;