rs7712007

Positions:

• chr5-163124746-A-T

Variant summary

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

The ENST00000646617.1(ENSG00000254186):​n.323-35400T>A 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 0.085 in 152,268 control chromosomes in the GnomAD database, including 605 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 0.085 (605 hom., cov: 33)
• Consequence: ENST00000646617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377700	XR_001742961.2	n.1374-35400T>A		intron_variant, non_coding_transcript_variant
LOC105377700	XR_002956233.2	n.1426-35400T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646617.1	n.323-35400T>A		intron_variant, non_coding_transcript_variant
	ENST00000509211.1	n.118-35400T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12940 AN: 152150 Hom.: 605 Cov.: 33

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.00904

Gnomad SAS AF: 0.0966

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0850 AC: 12947 AN: 152268 Hom.: 605 Cov.: 33 AF XY: 0.0844 AC XY: 6280 AN XY: 74440

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.0889

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.00887

Gnomad4 SAS AF: 0.0975

Gnomad4 FIN AF: 0.0786

Gnomad4 NFE AF: 0.0881

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.0803 Hom.: 66

Bravo AF: 0.0843

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7712007; hg19: chr5-162551752;