rs10498901

Variant names:

• chr6-74693065-G-A
• rs10498901
• ENST00000432484.6:n.199+41016C>T

Variant summary

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

The ENST00000432484.6(ENSG00000272243):​n.199+41016C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0181 in 152,152 control chromosomes in the GnomAD database, including 80 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 0.018 (80 hom., cov: 32)
• Consequence: ENSG00000272243 ENST00000432484.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 0 publications found

Genes affected

ENSG00000272243 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432484.6. 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
	LOC105377858	NR_187974.1		n.285+41016C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272243	ENST00000432484.6	TSL:3	n.199+41016C>T		intron	N/A
	ENSG00000272243	ENST00000658108.2		n.323+41016C>T		intron	N/A
	ENSG00000272243	ENST00000668767.1		n.199+41016C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0181 AC: 2752 AN: 152036 Hom.: 80 Cov.: 32

Gnomad AFR AF: 0.00326

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0224

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.0205

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

GnomAD4 genome AF: 0.0181 AC: 2750 AN: 152152 Hom.: 80 Cov.: 32 AF XY: 0.0202 AC XY: 1506 AN XY: 74374

African (AFR) AF: 0.00325 AC: 135 AN: 41560

American (AMR) AF: 0.0333 AC: 508 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3472

East Asian (EAS) AF: 0.138 AC: 713 AN: 5158

South Asian (SAS) AF: 0.0587 AC: 283 AN: 4822

European-Finnish (FIN) AF: 0.0224 AC: 237 AN: 10590

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0116 AC: 788 AN: 67972

Other (OTH) AF: 0.0208 AC: 44 AN: 2116

Alfa AF: 0.0139 Hom.: 4

Bravo AF: 0.0175

Asia WGS AF: 0.0810 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.66
PhyloP100		-2.2

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: rs10498901;

hg19: chr6-75402781;

COSMIC: COSV71363295;