rs10498901

chr6-74693065-G-A

Variant summary

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

The ENST00000432484.6(ENSG00000272243):n.199+41016C>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 0.0181 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: ENST00000432484.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377858	XR_942693.4	n.239+41016C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000432484.6	n.199+41016C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000658108.1	n.239+41016C>T		intron_variant, non_coding_transcript_variant
	ENST00000668767.1	n.199+41016C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00325

Gnomad4 AMR AF: 0.0333

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0587

Gnomad4 FIN AF: 0.0224

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.0208

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.12
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498901; hg19: chr6-75402781; COSMIC: COSV71363295;