rs1543851

chr7-65341359-A-Gchr7-65341359-A-T

Variant summary

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

The XR_001744938.2(LOC105375334):n.5416+2743A>G 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 0.298 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_001744938.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

LOC105375334 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375334	XR_001744938.2	n.5416+2743A>G		intron_variant, non_coding_transcript_variant
LOC105375334	XR_001744935.2	n.3571A>G		non_coding_transcript_exon_variant	5/5
LOC105375334	XR_007060361.1	n.8059A>G		non_coding_transcript_exon_variant	7/7
LOC105375334	XR_927613.3	n.828+2743A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.308

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1543851; hg19: chr7-64806272;