rs11973012

Variant names:

• chr7-127533608-T-C
• rs11973012
• ENST00000731796.1:n.70-28242A>G

Variant summary

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

The ENST00000731796.1(ENSG00000295686):​n.70-28242A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0794 in 152,254 control chromosomes in the GnomAD database, including 575 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 0.079 (575 hom., cov: 32)
• Consequence: ENSG00000295686 ENST00000731796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.945
• Publications: 6 publications found

Genes affected

ENSG00000295686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0983 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731796.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295686	ENST00000731796.1		n.70-28242A>G		intron	N/A
	ENSG00000295686	ENST00000731797.1		n.354+42069A>G		intron	N/A
	ENSG00000295686	ENST00000731798.1		n.243+1541A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12092 AN: 152136 Hom.: 575 Cov.: 32

Gnomad AFR AF: 0.0331

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0729

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.0948

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0794 AC: 12089 AN: 152254 Hom.: 575 Cov.: 32 AF XY: 0.0806 AC XY: 6001 AN XY: 74442

African (AFR) AF: 0.0331 AC: 1376 AN: 41554

American (AMR) AF: 0.0729 AC: 1115 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.0944 AC: 489 AN: 5178

South Asian (SAS) AF: 0.104 AC: 500 AN: 4824

European-Finnish (FIN) AF: 0.128 AC: 1358 AN: 10602

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6822 AN: 68014

Other (OTH) AF: 0.0734 AC: 155 AN: 2112

Alfa AF: 0.0861 Hom.: 100

Bravo AF: 0.0727

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.43
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs11973012; hg19: chr7-127173662;