rs4943770

Variant names:

• chr13-40336251-C-A
• rs4943770
• ENST00000400432.4:n.559+7706G>T

Your query was ambiguous. Multiple possible variants found:

• chr13-40336251-C-A
• chr13-40336251-C-T

Variant summary

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

The ENST00000654662.1(LINC00598):​n.552+7706G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,036 control chromosomes in the GnomAD database, including 21,365 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 0.52 (21365 hom., cov: 32)
• Consequence: LINC00598 ENST00000654662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 4 publications found

Genes affected

LINC00598 (HGNC:42770): (long intergenic non-protein coding RNA 598)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654662.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00598	ENST00000400432.4	TSL:5	n.559+7706G>T		intron	N/A
	LINC00598	ENST00000636192.2	TSL:5	n.620+7706G>T		intron	N/A
	LINC00598	ENST00000637438.1	TSL:5	n.205+13858G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79153 AN: 151920 Hom.: 21336 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.521 AC: 79214 AN: 152036 Hom.: 21365 Cov.: 32 AF XY: 0.530 AC XY: 39354 AN XY: 74320

African (AFR) AF: 0.384 AC: 15930 AN: 41450

American (AMR) AF: 0.654 AC: 9993 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1770 AN: 3472

East Asian (EAS) AF: 0.825 AC: 4269 AN: 5174

South Asian (SAS) AF: 0.580 AC: 2799 AN: 4822

European-Finnish (FIN) AF: 0.595 AC: 6294 AN: 10572

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.536 AC: 36430 AN: 67966

Other (OTH) AF: 0.534 AC: 1124 AN: 2104

Alfa AF: 0.518 Hom.: 7740

Bravo AF: 0.523

Asia WGS AF: 0.697 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.39
PhyloP100		-0.082

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4943770;

hg19: chr13-40910388;