rs7535849

Variant names:

• chr1-196131884-A-G
• rs7535849
• ENST00000838209.1:n.130+28486T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-196131884-A-G
• chr1-196131884-A-T

Variant summary

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

The ENST00000838209.1(LINC01724):​n.130+28486T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,004 control chromosomes in the GnomAD database, including 2,201 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 0.16 (2201 hom., cov: 32)
• Consequence: LINC01724 ENST00000838209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876
• Publications: 1 publications found

Genes affected

LINC01724 (HGNC:52512): (long intergenic non-protein coding RNA 1724)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838209.1. 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
	LINC01724	ENST00000838209.1		n.130+28486T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24320 AN: 151886 Hom.: 2197 Cov.: 32

Gnomad AFR AF: 0.0869

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.160 AC: 24335 AN: 152004 Hom.: 2201 Cov.: 32 AF XY: 0.164 AC XY: 12183 AN XY: 74316

African (AFR) AF: 0.0868 AC: 3602 AN: 41512

American (AMR) AF: 0.153 AC: 2340 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3468

East Asian (EAS) AF: 0.167 AC: 865 AN: 5170

South Asian (SAS) AF: 0.272 AC: 1308 AN: 4808

European-Finnish (FIN) AF: 0.240 AC: 2534 AN: 10558

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12303 AN: 67908

Other (OTH) AF: 0.176 AC: 371 AN: 2112

Alfa AF: 0.167 Hom.: 364

Bravo AF: 0.149

Asia WGS AF: 0.248 AC: 859 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.78
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs7535849; hg19: chr1-196101014;