rs7711912

chr5-171493699-A-Gchr5-171493699-A-T

Variant summary

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

The XR_941213.2(LOC105377721):n.132+1756T>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 0.482 in 151,574 control chromosomes in the GnomAD database, including 18,366 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 0.48 (18366 hom., cov: 30)
• Consequence: LOC105377721 XR_941213.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

Genes affected

LOC105377721 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377721	XR_941213.2	n.132+1756T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72902 AN: 151456 Hom.: 18317 Cov.: 30

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.482 AC: 73009 AN: 151574 Hom.: 18366 Cov.: 30 AF XY: 0.479 AC XY: 35494 AN XY: 74056

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.483

Alfa AF: 0.430 Hom.: 28299

Bravo AF: 0.491

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.8
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7711912; hg19: chr5-170920703;