rs4960710

Variant names:

• chr7-155244521-A-G
• rs4960710
• XR_007060608.1:n.4491T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007060608.1(LOC105375587):​n.4491T>C variant causes a non coding transcript exon 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: LOC105375587 XR_007060608.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 2 publications found

Genes affected

LOC105375587 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702445.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290007	ENST00000702445.2		n.187-805T>C		intron	N/A
	ENSG00000290007	ENST00000757102.1		n.83-805T>C		intron	N/A

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

African (AFR) AF: 0.478 AC: 19669 AN: 41182

American (AMR) AF: 0.295 AC: 4453 AN: 15090

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1496 AN: 3454

East Asian (EAS) AF: 0.0131 AC: 61 AN: 4674

South Asian (SAS) AF: 0.262 AC: 1178 AN: 4496

European-Finnish (FIN) AF: 0.374 AC: 3792 AN: 10144

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.415 AC: 28001 AN: 67518

Other (OTH) AF: 0.393 AC: 823 AN: 2094

Alfa AF: 0.398 Hom.: 16787

Bravo AF: 0.390

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.021
DANN	Benign	0.58
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4960710; hg19: chr7-155036231;