rs12666416

Variant names:

• chr7-12002791-A-G
• rs12666416
• ENST00000775347.1:n.290+91862T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-12002791-A-G
• chr7-12002791-A-T

Variant summary

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

The ENST00000775347.1(ENSG00000300984):​n.290+91862T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,818 control chromosomes in the GnomAD database, including 18,099 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 0.48 (18099 hom., cov: 32)
• Consequence: ENSG00000300984 ENST00000775347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 0 publications found

Genes affected

ENSG00000300984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901589	XR_007060211.1	n.85+91862T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300984	ENST00000775347.1	n.290+91862T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73350 AN: 151698 Hom.: 18090 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.483 AC: 73390 AN: 151818 Hom.: 18099 Cov.: 32 AF XY: 0.490 AC XY: 36330 AN XY: 74166

African (AFR) AF: 0.408 AC: 16920 AN: 41444

American (AMR) AF: 0.518 AC: 7892 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1587 AN: 3470

East Asian (EAS) AF: 0.708 AC: 3645 AN: 5146

South Asian (SAS) AF: 0.622 AC: 3004 AN: 4828

European-Finnish (FIN) AF: 0.541 AC: 5708 AN: 10548

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 32957 AN: 67856

Other (OTH) AF: 0.484 AC: 1017 AN: 2100

Alfa AF: 0.469 Hom.: 17725

Bravo AF: 0.475

Asia WGS AF: 0.674 AC: 2338 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.39
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs12666416; hg19: chr7-12042417;