rs11971309

Variant names:

• chr7-137027408-C-T
• rs11971309
• ENST00000439694.6:n.655+4497G>A

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.655+4497G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,002 control chromosomes in the GnomAD database, including 7,766 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 0.30 (7766 hom., cov: 32)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985
• Publications: 2 publications found

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC349160	NR_046103.1	n.341+5386G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234352	ENST00000439694.6	n.655+4497G>A		intron_variant	Intron 3 of 3	1
ENSG00000234352	ENST00000425981.2	n.341+5386G>A		intron_variant	Intron 2 of 3	2
ENSG00000234352	ENST00000586239.5	n.273+5386G>A		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45907 AN: 151884 Hom.: 7759 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.302 AC: 45932 AN: 152002 Hom.: 7766 Cov.: 32 AF XY: 0.299 AC XY: 22219 AN XY: 74270

African (AFR) AF: 0.190 AC: 7884 AN: 41506

American (AMR) AF: 0.271 AC: 4129 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3470

East Asian (EAS) AF: 0.0150 AC: 77 AN: 5128

South Asian (SAS) AF: 0.178 AC: 858 AN: 4820

European-Finnish (FIN) AF: 0.396 AC: 4186 AN: 10572

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26454 AN: 67940

Other (OTH) AF: 0.323 AC: 681 AN: 2106

Alfa AF: 0.352 Hom.: 5904

Bravo AF: 0.291

Asia WGS AF: 0.111 AC: 387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs11971309; hg19: chr7-136712155;