rs10511176

Positions:

• chr3-99607657-T-C

Variant summary

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

The ENST00000660954.1(ENSG00000244464):​n.395+9158T>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 0.0747 in 152,198 control chromosomes in the GnomAD database, including 502 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 0.075 (502 hom., cov: 33)
• Consequence: ENST00000660954.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 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
	ENST00000660954.1	n.395+9158T>C		intron_variant, non_coding_transcript_variant
	ENST00000462011.1	n.436+9158T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000655531.1	n.395+9158T>C		intron_variant, non_coding_transcript_variant
	ENST00000666141.1	n.411+9158T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0746 AC: 11344 AN: 152080 Hom.: 502 Cov.: 33

Gnomad AFR AF: 0.0973

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0495

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.0747 AC: 11363 AN: 152198 Hom.: 502 Cov.: 33 AF XY: 0.0767 AC XY: 5711 AN XY: 74414

Gnomad4 AFR AF: 0.0972

Gnomad4 AMR AF: 0.0928

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0601

Gnomad4 NFE AF: 0.0494

Gnomad4 OTH AF: 0.0943

Alfa AF: 0.0574 Hom.: 371

Bravo AF: 0.0785

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
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: rs10511176; hg19: chr3-99326501;