rs10486351

Positions:

• chr7-19497980-G-C

Variant summary

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

The ENST00000412563.1(ENSG00000223838):​n.357-78307G>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 0.0967 in 152,066 control chromosomes in the GnomAD database, including 1,437 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 0.097 (1437 hom., cov: 32)
• Consequence: ENST00000412563.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000412563.1	n.357-78307G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0965 AC: 14666 AN: 151948 Hom.: 1431 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0647

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0859

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

GnomAD4 genome AF: 0.0967 AC: 14706 AN: 152066 Hom.: 1437 Cov.: 32 AF XY: 0.0970 AC XY: 7210 AN XY: 74328

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0647

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.0570

Gnomad4 FIN AF: 0.0167

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.0845

Alfa AF: 0.0645 Hom.: 106

Bravo AF: 0.109

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486351; hg19: chr7-19537603;