4-181699071-T-G

Position:

• chr4-181699071-T-G

Variant summary

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

The ENST00000670601.1(ENSG00000287948):​n.124+948A>C 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 0.475 in 151,828 control chromosomes in the GnomAD database, including 18,204 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 0.47 (18204 hom., cov: 31)
• Consequence: ENST00000670601.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TENM3	XM_017008385.2	c.-399-40416T>G		intron_variant			XP_016863874.1
TENM3	XM_017008389.2	c.-399-40416T>G		intron_variant			XP_016863878.1
TENM3	XM_017008390.2	c.-399-40416T>G		intron_variant			XP_016863879.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000670601.1	n.124+948A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72031 AN: 151710 Hom.: 18187 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.475 AC: 72092 AN: 151828 Hom.: 18204 Cov.: 31 AF XY: 0.473 AC XY: 35129 AN XY: 74214

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.478

Alfa AF: 0.545 Hom.: 10547

Bravo AF: 0.448

Asia WGS AF: 0.396 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.18
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726856; hg19: chr4-182620224;