chr6-97319715-G-A

Variant names:

• chr6-97319715-G-A
• rs10499012
• ENST00000433637.2:n.460+13619G>A

Variant summary

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

The ENST00000433637.2(ENSG00000271860):​n.460+13619G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.061 in 152,202 control chromosomes in the GnomAD database, including 1,272 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 0.061 (1272 hom., cov: 32)
• Consequence: ENSG00000271860 ENST00000433637.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606
• Publications: 1 publications found

Genes affected

ENSG00000271860 (HGNC:58964):

LOC101927314 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433637.2. 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
	LOC101927314	NR_110757.1		n.511+13619G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000271860	ENST00000433637.2	TSL:2	n.460+13619G>A		intron	N/A
	ENSG00000271860	ENST00000457513.2	TSL:3	n.405+13619G>A		intron	N/A
	ENSG00000271860	ENST00000574739.2	TSL:4	n.505+13619G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0609 AC: 9255 AN: 152086 Hom.: 1260 Cov.: 32

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00594

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0610 AC: 9282 AN: 152202 Hom.: 1272 Cov.: 32 AF XY: 0.0684 AC XY: 5090 AN XY: 74406

African (AFR) AF: 0.0441 AC: 1830 AN: 41532

American (AMR) AF: 0.227 AC: 3462 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3470

East Asian (EAS) AF: 0.502 AC: 2593 AN: 5168

South Asian (SAS) AF: 0.0756 AC: 364 AN: 4816

European-Finnish (FIN) AF: 0.0417 AC: 442 AN: 10598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00594 AC: 404 AN: 68018

Other (OTH) AF: 0.0639 AC: 135 AN: 2114

Alfa AF: 0.0390 Hom.: 1577

Bravo AF: 0.0810

Asia WGS AF: 0.249 AC: 863 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	3.1
DANN	Benign	0.67
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs10499012; hg19: chr6-97767591;