NM_001142556.2:c.1269-110G>A

Variant names:

• chr5-163478574-G-A
• rs13183712
• NM_001142556.2:c.1269-110G>A

Variant summary

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

The NM_001142556.2(HMMR):​c.1269-110G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000182 in 548,044 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)
  • Exomes 𝑓: 0.0000018 (0 hom.)
• Consequence: HMMR NM_001142556.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 0 publications found

Genes affected

HMMR (HGNC:5012): (hyaluronan mediated motility receptor) The protein encoded by this gene is involved in cell motility. It is expressed in breast tissue and together with other proteins, it forms a complex with BRCA1 and BRCA2, thus is potentially associated with higher risk of breast cancer. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Dec 2008]

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=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142556.2. 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
	HMMR	NM_001142556.2	MANE Select	c.1269-110G>A		intron	N/A	NP_001136028.1	O75330-3
	HMMR	NM_012484.3		c.1266-110G>A		intron	N/A	NP_036616.2	O75330-1
	HMMR	NM_012485.3		c.1221-110G>A		intron	N/A	NP_036617.2	O75330-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMMR	ENST00000393915.9	TSL:1 MANE Select	c.1269-110G>A		intron	N/A	ENSP00000377492.4	O75330-3
	HMMR	ENST00000358715.3	TSL:1	c.1266-110G>A		intron	N/A	ENSP00000351554.3	O75330-1
	HMMR	ENST00000353866.7	TSL:1	c.1221-110G>A		intron	N/A	ENSP00000185942.6	O75330-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000182 AC: 1 AN: 548044 Hom.: 0 AF XY: 0.00000338 AC XY: 1 AN XY: 295902

African (AFR) AF: 0.00 AC: 0 AN: 14950

American (AMR) AF: 0.00 AC: 0 AN: 32322

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16116

East Asian (EAS) AF: 0.0000290 AC: 1 AN: 34452

South Asian (SAS) AF: 0.00 AC: 0 AN: 56156

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45042

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2716

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 317050

Other (OTH) AF: 0.00 AC: 0 AN: 29240

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.59
PhyloP100		-0.22

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs13183712; hg19: chr5-162905580;