rs12641856

Positions:

• chr4-181688712-G-A
• chr4-181688712-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000670601.1(ENSG00000287948):​n.125-2069C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0655 in 152,286 control chromosomes in the GnomAD database, including 448 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 0.066 (448 hom., cov: 33)
• Consequence: ENST00000670601.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM3	XM_017008385.2	c.-399-50775G>A		intron_variant
TENM3	XM_017008389.2	c.-399-50775G>A		intron_variant
TENM3	XM_017008390.2	c.-399-50775G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670601.1	n.125-2069C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0656 AC: 9977 AN: 152168 Hom.: 447 Cov.: 33

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0862

Gnomad OTH AF: 0.0745

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

GnomAD4 genome AF: 0.0655 AC: 9982 AN: 152286 Hom.: 448 Cov.: 33 AF XY: 0.0666 AC XY: 4957 AN XY: 74444

Gnomad4 AFR AF: 0.0162

Gnomad4 AMR AF: 0.0493

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0647

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0856

Gnomad4 NFE AF: 0.0862

Gnomad4 OTH AF: 0.0742

Alfa AF: 0.0646 Hom.: 178

Bravo AF: 0.0592

Asia WGS AF: 0.0980 AC: 340 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12641856; hg19: chr4-182609865;