rs12601191

Variant names:

• chr17-40951857-A-C
• rs12601191
• ENST00000418393.1:n.385+23175A>C

Your query was ambiguous. Multiple possible variants found:

• chr17-40951857-A-C
• chr17-40951857-A-T

Variant summary

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

The ENST00000418393.1(ENSG00000234477):​n.385+23175A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,066 control chromosomes in the GnomAD database, including 4,429 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 0.23 (4429 hom., cov: 32)
• Consequence: ENSG00000234477 ENST00000418393.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 6 publications found

Genes affected

ENSG00000234477 (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 (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985072	XR_001752885.2	n.80+23175A>C		intron_variant	Intron 1 of 2
LOC107985072	XR_001752886.2	n.80+23175A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234477	ENST00000418393.1	n.385+23175A>C		intron_variant	Intron 3 of 3	5
ENSG00000306126	ENST00000815517.1	n.60+15512A>C		intron_variant	Intron 1 of 2
ENSG00000234477	ENST00000815628.1	n.326+5470A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34985 AN: 151948 Hom.: 4423 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.230 AC: 35020 AN: 152066 Hom.: 4429 Cov.: 32 AF XY: 0.234 AC XY: 17374 AN XY: 74342

African (AFR) AF: 0.317 AC: 13135 AN: 41454

American (AMR) AF: 0.271 AC: 4145 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3472

East Asian (EAS) AF: 0.191 AC: 989 AN: 5180

South Asian (SAS) AF: 0.301 AC: 1450 AN: 4818

European-Finnish (FIN) AF: 0.185 AC: 1948 AN: 10556

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11642 AN: 67970

Other (OTH) AF: 0.250 AC: 530 AN: 2116

Alfa AF: 0.130 Hom.: 330

Bravo AF: 0.239

Asia WGS AF: 0.269 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.52
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs12601191; hg19: chr17-39108109;