7-65341359-A-T

Variant names:

• chr7-65341359-A-T
• rs1543851
• XR_001744935.2:n.3571A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XR_001744935.2(LOC105375334):​n.3571A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: LOC105375334 XR_001744935.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 6 publications found

Genes affected

LOC105375334 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375334	XR_001744935.2	n.3571A>T		non_coding_transcript_exon_variant	Exon 5 of 5
LOC105375334	XR_007060361.1	n.8059A>T		non_coding_transcript_exon_variant	Exon 7 of 7
LOC105375334	XR_001744938.2	n.5416+2743A>T		intron_variant	Intron 6 of 6
LOC105375334	XR_927613.3	n.828+2743A>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282381	ENST00000824229.1	n.551+2743A>T		intron_variant	Intron 3 of 3
ENSG00000282381	ENST00000824230.1	n.458+2743A>T		intron_variant	Intron 3 of 4
ENSG00000282381	ENST00000824231.1	n.520+2743A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 1069

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.78
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1543851; hg19: chr7-64806272;