rs1543851

Variant names:

• chr7-65341359-A-G
• rs1543851
• XR_001744935.2:n.3571A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-65341359-A-G
• chr7-65341359-A-T

Variant summary

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

The XR_001744935.2(LOC105375334):​n.3571A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 151,856 control chromosomes in the GnomAD database, including 7,783 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 0.30 (7783 hom., cov: 31)
• Consequence: LOC105375334 XR_001744935.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 6 publications found

Genes affected

LOC105375334 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375334	XR_001744935.2	n.3571A>G		non_coding_transcript_exon_variant	Exon 5 of 5
LOC105375334	XR_007060361.1	n.8059A>G		non_coding_transcript_exon_variant	Exon 7 of 7
LOC105375334	XR_001744938.2	n.5416+2743A>G		intron_variant	Intron 6 of 6
LOC105375334	XR_927613.3	n.828+2743A>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282381	ENST00000824229.1	n.551+2743A>G		intron_variant	Intron 3 of 3
ENSG00000282381	ENST00000824230.1	n.458+2743A>G		intron_variant	Intron 3 of 4
ENSG00000282381	ENST00000824231.1	n.520+2743A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45308 AN: 151736 Hom.: 7775 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.298 AC: 45322 AN: 151856 Hom.: 7783 Cov.: 31 AF XY: 0.296 AC XY: 21988 AN XY: 74228

African (AFR) AF: 0.143 AC: 5923 AN: 41430

American (AMR) AF: 0.261 AC: 3982 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1052 AN: 3466

East Asian (EAS) AF: 0.362 AC: 1873 AN: 5170

South Asian (SAS) AF: 0.388 AC: 1869 AN: 4812

European-Finnish (FIN) AF: 0.344 AC: 3614 AN: 10520

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25968 AN: 67912

Other (OTH) AF: 0.308 AC: 649 AN: 2106

Alfa AF: 0.325 Hom.: 1069

Bravo AF: 0.282

Asia WGS AF: 0.370 AC: 1281 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	13
DANN	Benign	0.74
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1543851; hg19: chr7-64806272;