rs7147817

Positions:

• chr14-40362800-A-G

Variant summary

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

The ENST00000652126.1(ENSG00000258526):​n.643-8721A>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 0.48 in 151,940 control chromosomes in the GnomAD database, including 18,117 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 (18117 hom., cov: 31)
• Consequence: ENST00000652126.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370462	XR_007064129.1	n.196-8721A>G		intron_variant, non_coding_transcript_variant
LOC105370462	XR_943784.3	n.192-8721A>G		intron_variant, non_coding_transcript_variant
LOC105370462	XR_943785.3	n.729+6816A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652126.1	n.643-8721A>G		intron_variant, non_coding_transcript_variant
	ENST00000553464.2	n.501-23452A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000663500.1	n.481-23452A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72927 AN: 151822 Hom.: 18111 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.480 AC: 72957 AN: 151940 Hom.: 18117 Cov.: 31 AF XY: 0.478 AC XY: 35529 AN XY: 74260

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.490

Alfa AF: 0.515 Hom.: 22210

Bravo AF: 0.470

Asia WGS AF: 0.317 AC: 1100 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7147817; hg19: chr14-40832004;