rs4960710

Positions:

• chr7-155244521-A-G
• chr7-155244521-A-T

Variant summary

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

The ENST00000702445.1(ENSG00000290007):​n.184-805T>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 0.4 in 149,838 control chromosomes in the GnomAD database, including 12,558 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 0.40 (12558 hom., cov: 31)
• Consequence: ENST00000702445.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375587	XR_001745437.2	n.1712-805T>C		intron_variant, non_coding_transcript_variant
LOC105375587	XR_007060608.1	n.4491T>C		non_coding_transcript_exon_variant	2/4
LOC105375587	XR_001745438.2	n.143-805T>C		intron_variant, non_coding_transcript_variant
LOC105375587	XR_928226.2	n.157-805T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000702445.1	n.184-805T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.400 AC: 59874 AN: 149718 Hom.: 12540 Cov.: 31

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.0130

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.400 AC: 59918 AN: 149838 Hom.: 12558 Cov.: 31 AF XY: 0.392 AC XY: 28719 AN XY: 73180

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.393

Alfa AF: 0.397 Hom.: 12972

Bravo AF: 0.390

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.021
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4960710; hg19: chr7-155036231;